Logging upgrade has disabled realtime optimization feedback for most functions #63
Description
Many functions in bigstream.align and bigstream.transform must report optimization performance to the user in realtime. Previously these reports were given with print. This was swapped out for logging, which in principle is good, but all these messages were set at level.DEBUG. The temporary fix for seeing these outputs is to do:
from bigstream.configure_bigstream import configure_logging
logger = configure_logging(None, True)
at the beginning of any cell or script that uses a function for which you need print feedback. However I have found that sometimes the logger fails for reason I don't understand (see stack trace) and when it does work, this sets all loggers for every function to the same output handlers. This mixes outputs for multiple functions making the output difficult to parse visually.
Overall, the logging system needs to be more carefully set up with the right outputs going to the right places at the right times, where the user can control these choices at run time. The logging system needs to be set up to accommodate users who interact with bigstream via the python module first, since this is the majority of users.
I can help with these changes.